π–π Stacking Interaction of Metal Phenoxyl Radical Complexes

π–π stacking interaction is well-known to be one of the weak interactions. Its importance in the stabilization of protein structures and functionalization has been reported for various systems. We have focused on a single copper oxidase, galactose oxidase, which has the π–π stacking interaction of the alkylthio-substituted phenoxyl radical with the indole ring of the proximal tryptophan residue and catalyzes primary alcohol oxidation to give the corresponding aldehyde. This stacking interaction has been considered to stabilize the alkylthio-phenoxyl radical, but further details of the interaction are still unclear. In this review, we discuss the effect of the π–π stacking interaction of the alkylthio-substituted phenoxyl radical with an indole ring.     

Cooperation of σ–π and σ*–π* Conjugation in the UV/Vis and Fluorescence Spectra of 9,10-Disilylanthracene

In 1996, we reported that silyl groups of 9,10-disilylanthracenes significantly affect the UV/Vis and fluorescence spectra. Although the results indicate that the silyl groups have strong electronic effects on anthracene, the details of the mechanisms responsible for this have not yet been clarified. This article describes the analysis of the UV/Vis and fluorescence spectra of 9,10-bis(diisopropylsilyl)anthracene by theoretical calculations. This study reveals that π conjugation of anthracene is extended by cooperation of σ–π and σ*–π* conjugation between the silyl groups and anthracene. This effect increases the transition moment of the π–π* transition of anthracene. As a result, the molecular extinction coefficient of the ¹L_a band and the fluorescence quantum yield are increased.     

π–π Noncovalent Interaction Involving 1,2,4- and 1,3,4-Oxadiazole Systems: The Combined Experimental,Theoretical, and Database Study

A series of N-pyridyl ureas bearing 1,2,4- (1a, 2a, and 3a) and 1,3,4-oxadiazole moiety (1b, 2b, 3b) was prepared and characterized by HRMS, ¹H and ¹³C NMR spectroscopy, as well as X-ray diffraction. The inspection of the crystal structures of (1–3)a,b and the Hirshfeld surface analysis made possible the recognition of the (oxadiazole)···(pyridine) and (oxadiazole)···(oxadiazole) interactions. The presence of these interactions was confirmed theoretically by DFT calculations, including NCI analysis for experimentally determined crystal structures as well as QTAIM analysis for optimized equilibrium structures. The preformed database survey allowed the verification of additional examples of relevant (oxadiazole)···π interactions both in Cambridge Structural Database and in Protein Data Bank, including the cocrystal of commercial anti-HIV drug Raltegravir.     

Janus-Type AIE Fluorophores: Synthesis and Properties of π-Extended Coumarin-Bearing Triskelions

Janus-type triskelion-shaped fluorophores comprising coumarins bearing various electron-donating substituents (1aad, 1add, 1ccd, and 1cdd) were successfully synthesized via an intramolecular Ullmann coupling. Density functional theory (DFT) calculations indicated that all the compounds presented two different molecular surfaces, similar to Janus-type molecules. The absorption and fluorescence spectra of asymmetrical derivatives 1aad, 1add, 1ccd, and 1cdd exhibited a bathochromic shift due to their narrow highest occupied molecular orbital (HOMO) –lowest unoccupied molecular orbital (LUMO) gap. Natural transition orbital (NTO) analysis indicated that the excited state orbital overlaps differ among the C₃ symmetrical and asymmetrical dyes. These triskelion-shaped fluorophores were found to form molecular nanoaggregates in THF/H₂O mixtures and demonstrated aggregation-induced emission (AIE) enhancement characteristics as a result of restricting their molecular inversion. These results indicate that Janus-type AIE fluorophores are potentially applicable as solid-state fluorescent chiral materials, which can be optimized by controlling their molecular rearrangement in the solid state.     

A–X⋯σ Interactions—Halogen Bonds with σ-Electrons as the Lewis Base Centre

CCSD(T)/aug-cc-pVTZ//ωB97XD/aug-cc-pVTZ calculations were performed for halogen-bonded complexes. Here, the molecular hydrogen, cyclopropane, cyclobutane and cyclopentane act as Lewis base units that interact through the electrons of the H–H or C–C σ-bond. The FCCH, ClCCH, BrCCH and ICCH species, as well as the F₂, Cl₂, Br₂ and I₂ molecular halogens, act as Lewis acid units in these complexes, interacting through the σ-hole localised at the halogen centre. The Quantum Theory of Atoms in Molecules (QTAIM), the Natural Bond Orbital (NBO) and the Energy Decomposition Analysis (EDA) approaches were applied to analyse these aforementioned complexes. These complexes may be classified as linked by A–X···σ halogen bonds, where A = C, X (halogen). However, distinct properties of these halogen bonds are observed that depend partly on the kind of electron donor: dihydrogen, cyclopropane, or another cycloalkane. Examples of similar interactions that occur in crystals are presented; Cambridge Structural Database (CSD) searches were carried out to find species linked by the A–X···σ halogen bonds.     

Insight into Spodium–π Bonding Characteristics of the MX2⋯π (M = Zn,Cd and Hg; X = Cl,Br and I) Complexes—A Theoretical Study

The spodium–π bonding between MX₂ (M = Zn, Cd, and Hg; X = Cl, Br, and I) acting as a Lewis acid, and C₂H₂/C₂H₄ acting as a Lewis base was studied by ab initio calculations. Two types of structures of cross (T) and parallel (P) forms are obtained. For the T form, the X–M–X axis adopts a cross configuration with the molecular axis of C≡C or C=C, but both of them are parallel in the P form. NCI, AIM, and electron density shifts analyses further, indicating that the spodium–π bonding exists in the binary complexes. Spodium–π bonding exhibits a partially covalent nature characterized with a negative energy density and large interaction energy. With the increase of electronegativity of the substituents on the Lewis acid or its decrease in the Lewis base, the interaction energies increase and vice versa. The spodium–π interaction is dominated by electrostatic interaction in most complexes, whereas dispersion and electrostatic energies are responsible for the stability of the MX₂⋯C₂F₂ complexes. The spodium–π bonding further complements the concept of the spodium bond and provides a wider range of research on the adjustment of the strength of spodium bond.     

Synthesis and Characterization of Vanillin-Based π-Conjugated Polyazomethines and Their Oligomer Model Compounds

The synthesis of π-conjugated polymers via an environmentally friendly procedure is generally challenging. Herein, we describe the synthesis of divanillin-based polyazomethines, which are derived from a potentially bio-based monomer. The polymerization is performed in 5 min under microwave irradiation without any metallic catalyst, with water as the only by-product. The vanillin-based polyazomethines were characterized by SEC, TGA, and UV-Vis spectroscopy. Model compounds were designed and characterized by X-ray diffraction and UV-Vis spectroscopy. The structure/properties study of vanillin-based azomethines used as models allowed us to unequivocally confirm the E configuration and to highlight the cross-conjugated nature of divanillin-based polymers.     

Dual XH–π Interaction of Hexafluoroisopropanol with Arenes

The dual XH (OH and CH) hydrogen-bond-donating property of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) and the strong dual XH–π interaction with arenes were firstly disclosed by theoretical studies. Here, the high accuracy post-Hartree–Fock methods, CCSD(T)/CBS, reveal the interaction energy of HFIP/benzene complex (−7.22 kcal/mol) and the contribution of the electronic correlation energy in the total interaction energy. Strong orbital interaction between HFIP and benzene was found by using the DFT method in this work to disclose the dual XH–π intermolecular orbital interaction of HFIP with benzene-forming bonding and antibonding orbitals resulting from the orbital symmetry of HFIP. The density of states and charge decomposition analyses were used to investigate the orbital interactions. Isopropanol (IP), an analogue of HFIP, and chloroform (CHCl₃) were studied to compare them with the classical OH–π, and non-classical CH–π interactions. In addition, the influence of the aggregating effect of HFIP, and the numbers of substituted methyl groups in benzene rings were also studied. The interaction energies of HFIP with the selected 24 common organic compounds were calculated to understand the role of HFIP as solvent or additive in organic transformation in a more detailed manner. A single-crystal X-ray diffraction study of hexafluoroisopropyl benzoate further disclosed and confirmed that the CH of HFIP shows the non-classical hydrogen-bond-donating behavior.     

π-Stacking Stopper-Macrocycle Stabilized Dynamically Interlocked [2]Rotaxanes

The synthesis of mechanically interlocked molecules is valuable due to their unique topologies. With π-stacking intercomponent interaction, e.g., phenanthroline and anthracene, novel [2]rotaxanes have been synthesized by dynamic imine clipping reaction. Their X-ray crystal structures indicate the π-stackings between the anthracene moiety (stopper) on the thread and the (hetero)aromatic rings at the macrocycle of the rotaxanes. Moreover, the length of glycol chains affects the extra π-stacking intercomponent interactions between the phenyl groups and the dimethoxy phenyl groups on the thread. Dynamic combinatorial library has shown at best 84% distribution of anthracene-threaded phenanthroline-based rotaxane, coinciding with the crystallography in that the additional π-stacking intercomponent interactions could increase the thermodynamic stability and selectivity of the rotaxanes.     

Density Functional Method Study on the Cooperativity of Intermolecular H-bonding and π-π+ Stacking Interactions in Thymine-[Cnmim]Br (n = 2, 4, 6, 8, 10) Microhydrates

The exploration of the ionic liquids’ mechanism of action on nucleobase’s structure and properties is still limited. In this work, the binding model of the 1-alkyl-3-methylimidazolium bromide ([C_nmim]Br, n = 2, 4, 6, 8, 10) ionic liquids to the thymine (T) was studied in a water environment (PCM) and a microhydrated surroundings (PCM + wH₂O). Geometries of the mono-, di-, tri-, and tetra-ionic thymine (T-wH₂O-y[C_nmim]⁺-xBr⁻, w = 5~1 and x + y = 0~4) complexes were optimized at the M06-2X/6-311++G(2d, p) level. The IR and UV-Vis spectra, QTAIM, and NBO analysis for the most stable T-4H₂O-Br⁻-1, T-3H₂O-[C_nmim]⁺-Br⁻-1, T-2H₂O-[C_nmim]⁺-2Br⁻-1, and T-1H₂O-2[C_nmim]⁺-2Br⁻-1 hydrates were presented in great detail. The results show that the order of the arrangement stability of thymine with the cations (T-[C_nmim]⁺) by PCM is stacking > perpendicular > coplanar, and with the anion (T-Br⁻) is front > top. The stability order for the different microhydrates is following T-5H₂O-1 < T-4H₂O-Br⁻-1 < T-3H₂O-[C_nmim]⁺-Br⁻-1 < T-2H₂O-[C_nmim]⁺-2Br⁻-1 < T-1H₂O-2[C_nmim]⁺-2Br⁻-1. A good linear relationship between binding E_B values and the increasing number (x + y) of ions has been found, which indicates that the cooperativity of interactions for the H-bonding and π-π⁺ stacking is varying incrementally in the growing ionic clusters. The stacking model between thymine and [C_nmim]⁺ cations is accompanied by weaker hydrogen bonds which are always much less favorable than those in T-xBr⁻ complexes; the same trend holds when the clusters in size grow and the length of alkyl chains in the imidazolium cations increase. QTAIM and NBO analytical methods support the existence of mutually reinforcing hydrogen bonds and π-π cooperativity in the systems.     

Intermolecular CH-π Electrons Interaction in Poly (9,9-dioctylfluorenyl-2,7-diyl) (PFO): An Experimental and Theoretical Study

This study demonstrates the presence of CH-π interaction in poly [9,9-dioctylfluorenyl-2,7-diyl] (PFO-1) due to an aggregate formation of PFO-1 in the liquid state. The absorption spectra of PFO-1 in certain solvents at low concentrations showed a single band at 390 nm. However, when using high concentrations, a new band at 437 nm appeared. This band is due to the aggregate formation of PFO-1. The aggregate formation occurs as a result of the CH interaction of the n-alkyl side chains with π-electrons in the benzene ring. The optical characteristics of another conjugated polymer of poly [9,9-di-(2-ethylhexyl)-fluorenyl-2,7-diyl] (PFO-2) were investigated to confirm the CH-π interaction. The absorption showed only one wavelength at 390 nm without any new band at the end of the spectrum, even at higher concentrations and lower temperatures. The main reason for the absence of aggregate formation in PFO-2 is the sterical hindrance caused by the branched alkyl side chains. In addition, Density Functional Theory (DFT) was used to compute the HOMO–LUMO transitions, electron charge distribution, and frontier molecular orbitals for each polymer. The Mulliken charge distribution and demonstrated a notable difference in the reactivity of the alkyl side chain, confirming the higher ability of PFO-1 to form CH-π bonds. docking model emphasized that the band at 437 nm could be attributed to the interaction between CH in the n-alkyl side chain and π bonds in the aromatic rings of PFO-1.     

The Bifurcated σ-Hole···σ-Hole Stacking Interactions

The bifurcated σ-hole···σ-hole stacking interactions between organosulfur molecules, which are key components of organic optical and electronic materials, were investigated by using a combined method of the Cambridge Structural Database search and quantum chemical calculation. Due to the geometric constraints, the binding energy of one bifurcated σ-hole···σ-hole stacking interaction is in general smaller than the sum of the binding energies of two free monofurcated σ-hole···σ-hole stacking interactions. The bifurcated σ-hole···σ-hole stacking interactions are still of the dispersion-dominated noncovalent interactions. However, in contrast to the linear monofurcated σ-hole···σ-hole stacking interaction, the contribution of the electrostatic energy to the total attractive interaction energy increases significantly and the dispersion component of the total attractive interaction energy decreases significantly for the bifurcated σ-hole···σ-hole stacking interaction. Another important finding of this study is that the low-cost spin-component scaled zeroth-order symmetry-adapted perturbation theory performs perfectly in the study of the bifurcated σ-hole···σ-hole stacking interactions. This work will provide valuable information for the design and synthesis of novel organic optical and electronic materials.     

Spectroscopic and Theoretical Study of the Intramolecular π-Type Hydrogen Bonding and Conformations of 2-Cyclopenten-1-ol

The conformations of 2-cyclopenten-1-ol (2CPOL) have been investigated by high-level theoretical computations and infrared spectroscopy. The six conformational minima correspond to specific values of the ring-puckering and OH internal rotation coordinates. The conformation with the lowest energy possesses intramolecular π-type hydrogen bonding. A second conformer with weaker hydrogen bonding has somewhat higher energy. Ab initio coupled-cluster theory with single and double excitations (CCSD) was used with the cc-pVTZ (triple-ζ) basis set to calculate the two-dimensional potential energy surface (PES) governing the conformational dynamics along the ring-puckering and internal rotation coordinates. The two conformers with the hydrogen bonding lie about 300 cm⁻¹ (0.8 kcal/mole) lower in energy than the other four conformers. The lowest energy conformation has a calculated distance of 2.68 Å from the hydrogen atom on the OH group to the middle of the C=C double bond. For the other conformers, this distance is at least 0.3 Å longer. The infrared spectrum in the O-H stretching region agrees well with the predicted frequency differences between the conformers and shows the conformers with the hydrogen bonding to have the lowest values. The infrared spectra in other regions arise mostly from the two hydrogen-bonded species.     

Multispectral and Molecular Docking Studies Reveal Potential Effectiveness of Antidepressant Fluoxetine by Forming π-Acceptor Complexes

Poor mood, lack of pleasure, reduced focus, remorse, unpleasant thoughts, and sleep difficulties are all symptoms of depression. The only approved treatment for children and adolescents with major depressive disorder (MDD) is fluoxetine hydrochloride (FXN), a serotonin selective reuptake inhibitor antidepressant. MDD is the most common cause of disability worldwide. In the present research, picric acid (PA); dinitrobenzene; p-nitro benzoic acid; 2,6-dichloroquinone-4-chloroimide; 2,6-dibromoquinone-4-chloroimide; and 7,7′,8,8′-tetracyanoquinodimethane were used to make 1:1 FXN charge-transfer compounds in solid and liquid forms. The isolated complexes were then characterized by elemental analysis, conductivity, infrared, Raman, and ¹H-NMR spectra, thermogravimetric analysis, scanning electron microscopy, and X-ray powder diffraction. Additionally, a molecular docking investigation was conducted on the donor moiety using FXN alone and the resulting charge transfer complex [(FXN)(PA)] as an acceptor to examine the interactions against two protein receptors (serotonin or dopamine). Interestingly, the [(FXN)(PA)] complex binds to both serotonin and dopamine more effectively than the FXN drug alone. Furthermore, [(FXN)(PA)]–serotonin had a greater binding energy than [FXN]–serotonin. Theoretical data were also generated by density functional theory simulations, which aided the molecular geometry investigation and could be beneficial to researchers in the future.     

Interplay between Metal⋅⋅⋅π Interactions and Hydrogen Bonds: Some Unusual Synergetic Effects of Coinage Metals and Substituents

The ternary systems of C₂H₄ (C₂H₂ or C₆H₆)‐MCN‐HF (M=Cu, Ag, Au) and the respective binary systems were investigated to study the interplay between metal???π interactions and hydrogen bonds. The metal???π interactions in C₂H₄‐MCN become stronger with the irregular order Ag<Cu<Au, while the hydrogen bonds in MCN‐HF become weaker following the same order. The metal???π interactions are weakened as the H atoms in the π system are replaced with electron‐withdrawing groups and enhanced by electron‐donating groups. Type 1 of these ternary systems, in which MCN acts as Lewis base and acid simultaneously, is more stable than type 2, in which C₂H₄ acts as a double Lewis base. Negative cooperativity is present in type 2 ternary systems with a weakening of the metal???π interactions and the hydrogen bonds. Positive cooperativity is found in type 1 ternary systems with an enhancement of the metal???π interactions and the hydrogen bonds, except for C₂(CN)₄‐AuCN‐HF‐1. The weaker metal???π interaction in C₆H₆‐AuCN has a greater enhancing effect on the hydrogen bond in AuCN‐HF than those in C₂H₄‐AuCN and C₂H₂‐AuCN. These synergetic effects were analyzed with the natural bond orbital and energy decomposition.     

A comparative experimental and theoretical investigation of hydrogen‐bond,halogen‐bond and π–π interactions in the solid‐state supramolecular assembly of 2‐ and 4‐formylphenyl arylsulfonates

To explore the operational role of noncovalent interactions in supramolecular architectures with designed topologies, a series of solid‐state structures of 2‐ and 4‐formylphenyl 4‐substituted benzenesulfonates was investigated. The compounds are 2‐formylphenyl 4‐methylbenzenesulfonate, C₁₄H₁₂O₄S, 3a , 2‐formylphenyl 4‐chlorobenzenesulfonate, C₁₃H₉ClO₄S, 3b , 2‐formylphenyl 4‐bromobenzenesulfonate, C₁₃H₉BrO₄S, 3c , 4‐formylphenyl 4‐methylbenzenesulfonate, C₁₄H₁₂O₄S, 4a , 4‐formylphenyl 4‐chlorobenzenesulfonate, 4b , C₁₃H₉ClO₄S, and 4‐formylphenyl 4‐bromobenzenesulfonate, C₁₃H₉BrO₄S, 4c . The title compounds were synthesized under basic conditions from salicylaldehyde/4‐hydroxybenzaldehydes and various aryl sulfonyl chlorides. Remarkably, halogen‐bonding interactions are found to be important to rationalize the solid‐state crystal structures. In particular, the formation of O…X (X = Cl and Br) and type I X…X halogen‐bonding interactions have been analyzed by means of density functional theory (DFT) calculations and characterized using Bader's theory of `atoms in molecules' and molecular electrostatic potential (MEP) surfaces, confirming the relevance and stabilizing nature of these interactions. They have been compared to antiparallel π‐stacking interactions that are formed between the arylsulfonates.     

The peptide NCbz‐Val‐Tyr‐OMe and aromatic π–π interactions

The peptide N‐benzyloxycarbonyl‐L‐valyl‐L‐tyrosine methyl ester or NCbz‐Val‐Tyr‐OMe (where NCbz is N‐benzyloxycarbonyl and OMe indicates the methyl ester), C₂₃H₂₈N₂O₆, has an extended backbone conformation. The aromatic rings of the Tyr residue and the NCbz group are involved in various attractive intra‐ and intermolecular aromatic π–π interactions which stabilize the conformation and packing in the crystal structure, in addition to N—H...O and O—H...O hydrogen bonds. The aromatic π–π interactions include parallel‐displaced, perpendicular T‐shaped, perpendicular L‐shaped and inclined orientations.     

Construction of Hetero‐Four‐Layered Tripalladium(II) Cyclophanes by Transannular π⋅⋅⋅π Interactions

A synthetic strategy for the generation of new molecular species utilizing a provision of nature is presented. Nano‐dimensional (23(2)×21(1)×16(1) ų) hetero‐four‐layered trimetallacyclophanes were constructed by proof‐of‐concept experiments that utilize a suitable combination of π???π interactions between the central aromatic rings, tailor‐made short/long spacer tridentate donors, and the combined helicity. The behavior of the unprecedented four‐layered metallacyclophane system offers a landmark in the development of new molecular systems.     

The tropolone–isobutylamine complex: a hydrogen‐bonded troponoid without dominant π–π interactions

Tropolone long has served as a model system for unraveling the ubiquitous phenomena of proton transfer and hydrogen bonding. This molecule, which juxtaposes ketonic, hydroxylic, and aromatic functionalities in a framework of minimal complexity, also has provided a versatile platform for investigating the synergism among competing intermolecular forces, including those generated by hydrogen bonding and aryl coupling. Small members of the troponoid family typically produce crystals that are stabilized strongly by pervasive π–π, C—H…π, or ion–π interactions. The organic salt (TrOH·iBA) formed by a facile proton‐transfer reaction between tropolone (TrOH) and isobutylamine (iBA), namely isobutylammonium 7‐oxocyclohepta‐1,3,5‐trien‐1‐olate, C₄H₁₂N⁺·C₇H₅O₂⁻, has been investigated by X‐ray crystallography, with complementary quantum‐chemical and statistical‐database analyses serving to elucidate the nature of attendant intermolecular interactions and their synergistic effects upon lattice‐packing phenomena. The crystal structure deduced from low‐temperature diffraction measurements displays extensive hydrogen‐bonding networks, yet shows little evidence of the aryl forces (viz. π–π, C—H…π, and ion–π interactions) that typically dominate this class of compounds. Density functional calculations performed with and without the imposition of periodic boundary conditions (the latter entailing isolated subunits) documented the specificity and directionality of noncovalent interactions occurring between the proton‐donating and proton‐accepting sites of TrOH and iBA, as well as the absence of aromatic coupling mediated by the seven‐membered ring of TrOH. A statistical comparison of the structural parameters extracted for key hydrogen‐bond linkages to those reported for 44 previously known crystals that support similar binding motifs revealed TrOH·iBA to possess the shortest donor–acceptor distances of any troponoid‐based complex, combined with unambiguous signatures of enhanced proton‐delocalization processes that putatively stabilize the corresponding crystalline lattice and facilitate its surprisingly rapid formation under ambient conditions.